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BioC 3.3: CHECK report for BasicSTARRseq on moscato2

This page was generated on 2016-10-13 12:54:50 -0700 (Thu, 13 Oct 2016).

Package 78/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BasicSTARRseq 1.0.2
Annika Buerger
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BasicSTARRseq
Last Changed Rev: 118766 / Revision: 122332
Last Changed Date: 2016-06-20 06:43:30 -0700 (Mon, 20 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BasicSTARRseq
Version: 1.0.2
Command: rm -rf BasicSTARRseq.buildbin-libdir BasicSTARRseq.Rcheck && mkdir BasicSTARRseq.buildbin-libdir BasicSTARRseq.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BasicSTARRseq.buildbin-libdir BasicSTARRseq_1.0.2.tar.gz >BasicSTARRseq.Rcheck\00install.out 2>&1 && cp BasicSTARRseq.Rcheck\00install.out BasicSTARRseq-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BasicSTARRseq.buildbin-libdir --install="check:BasicSTARRseq-install.out" --force-multiarch --no-vignettes --timings BasicSTARRseq_1.0.2.tar.gz
StartedAt: 2016-10-13 01:13:16 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:16:42 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 206.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BasicSTARRseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BasicSTARRseq.buildbin-libdir BasicSTARRseq.Rcheck && mkdir BasicSTARRseq.buildbin-libdir BasicSTARRseq.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BasicSTARRseq.buildbin-libdir BasicSTARRseq_1.0.2.tar.gz >BasicSTARRseq.Rcheck\00install.out 2>&1 && cp BasicSTARRseq.Rcheck\00install.out BasicSTARRseq-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BasicSTARRseq.buildbin-libdir --install="check:BasicSTARRseq-install.out" --force-multiarch --no-vignettes --timings BasicSTARRseq_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/BasicSTARRseq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BasicSTARRseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BasicSTARRseq' version '1.0.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BasicSTARRseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPeaks,STARRseqData : <anonymous>: no visible global function
  definition for 'pbinom'
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbld/bbs-3.3-bioc/meat/BasicSTARRseq.Rcheck/00check.log'
for details.


BasicSTARRseq.Rcheck/00install.out:


install for i386

* installing *source* package 'BasicSTARRseq' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'sample' in package 'BasicSTARRseq'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'BasicSTARRseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BasicSTARRseq' as BasicSTARRseq_1.0.2.zip
* DONE (BasicSTARRseq)

BasicSTARRseq.Rcheck/examples_i386/BasicSTARRseq-Ex.timings:

nameusersystemelapsed
STARRseqData-class0.320.000.33
getPeaks0.780.000.78

BasicSTARRseq.Rcheck/examples_x64/BasicSTARRseq-Ex.timings:

nameusersystemelapsed
STARRseqData-class0.560.000.89
getPeaks0.890.000.88